Research workbench
Crystal structure of penicillin-binding protein 1 (PBP1) from staphylococcus aureus
Analyse Crystal structure of penicillin-binding protein 1 (PBP1) from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O49
- Type
- protein
- Length
- 6,153 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 1
- UniProt
- A0A0H2WVW5
- Ligands
- CD, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 11 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 1 | protein | 521 | 32% helix, 23% strand | A0A0H2WVW5 |
| B | Penicillin-binding protein 1 | protein | 527 | 32% helix, 23% strand | A0A0H2WVW5 |
| C, G | Penicillin-binding protein 1 | protein | 520 | 32% helix, 24% strand | A0A0H2WVW5 |
| D | Penicillin-binding protein 1 | protein | 502 | 32% helix, 24% strand | A0A0H2WVW5 |
| E | Penicillin-binding protein 1 | protein | 523 | 32% helix, 24% strand | A0A0H2WVW5 |
| F | Penicillin-binding protein 1 | protein | 528 | 31% helix, 23% strand | A0A0H2WVW5 |
| H | Penicillin-binding protein 1 | protein | 471 | 30% helix, 25% strand | A0A0H2WVW5 |
| I | Penicillin-binding protein 1 | protein | 518 | 32% helix, 24% strand | A0A0H2WVW5 |
| J | Penicillin-binding protein 1 | protein | 518 | 32% helix, 24% strand | A0A0H2WVW5 |
| K | Penicillin-binding protein 1 | protein | 511 | 31% helix, 24% strand | A0A0H2WVW5 |
| L | Penicillin-binding protein 1 | protein | 494 | 30% helix, 25% strand | A0A0H2WVW5 |
Ligands and binding sites
- CD · Cadmium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CL · Chloride ion · ion · 8 copies · chains C, D, E, F, H, J, K, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.86 | 0.90 | 121 | empty |
| 2 | 762 | 0.84 | 0.87 | 100 | empty |
| 3 | 939 | 0.84 | 0.85 | 125 | empty |
| 4 | 1013 | 0.83 | 0.84 | 119 | empty |
| 5 | 247 | 0.82 | 0.95 | 42 | empty |
Interfaces
20 interfaces between chains.
- C–K · 2301 Ų buried · 31 hydrogen bonds · protein-protein
- F–I · 2258 Ų buried · 26 hydrogen bonds · protein-protein
- J–L · 2147 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2103 Ų buried · 26 hydrogen bonds · protein-protein
- D–H · 1869 Ų buried · 27 hydrogen bonds · protein-protein
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A0H2WVW5
- Elsewhere: RCSB PDB 7O49 · PDBe 7O49 · UniProt A0A0H2WVW5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.